Caiwei at 22:14, 4 January 2009

2009-01-04T22:14:28Z

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	Forward Flux Sampling ~~(FFS)~~ of Rare Events in MD++</STRONG></font></P>		Forward Flux Sampling of Rare Events in MD++</STRONG></font></P>
	<DIV>		<DIV>
	<P ALIGN="CENTER"><STRONG>Seunghwa Ryu and Wei Cai</STRONG></P>		<P ALIGN="CENTER"><STRONG>Seunghwa Ryu and Wei Cai</STRONG></P>

Caiwei: initial import

2009-01-04T22:08:30Z

initial import

New page

Forward Flux Sampling (FFS) of Rare Events in MD++
<DIV>
Seunghwa Ryu and Wei Cai
</DIV>

This tutorial describes how to use Forward Flux Sampling (FFS) algorithm in MD++ to sample rare events (such as nucleation). The theoretical background is published in

Rosalind J. Allen, Daan Frenkel, and Pieter Rein ten Wolde, Simulating rare events in equilibrium or nonequilibrium stochastic systems, ''Journal of Chemical Physics'', '''124''', 024102 (2006).
<HR>

==Download files==

First, you need to install MD++ on your computer by following the instructions on [[MD++_Manuals | MD++ Manuals]].

Second, copy files ??? and ??? to your input file directory of MD++. You can do so by the following commands (assuming you have installed MD++ in <tt>~/Codes/MD++</tt>).

<pre>
export MDPP=~/Codes/MD++
mkdir -p ${MDPP}/scripts/work/melting
cd ${MDPP}/scripts/work/melting
wget ??? -O ???
wget ??? -O ???
</pre>

==Compile excutable file==

In this tutorial, we will study homogeneous nucleation of crystal from Si melt. Si will be modelled by the SW potential. The MD++ executable with SW potential can be compiled by the following command (on wcr.stanford.edu).

For example, you can compile <tt>sworig</tt> by typing
<pre>
cd ${MDPP}
make sw build=R SYS=wcr
</pre>
If compilation is successful, this will create binary file <tt>sw_wcr</tt> file in your <tt>${MDPP}/bin</tt> directory.

Please contact <tt>shryu@stanford.edu</tt> if you have further questions.

==Run simulations==

==Analyse data==

Nucleation rate of embryonic crystals.

Survival probability for the embryonic crystal to grow to larger (stable) size.

Foward Flux Sampling in MD++ - Revision history

Caiwei at 22:14, 4 January 2009

Caiwei: initial import